Data
load("./input/limma_SC_Controls.RData")
dea <- dea.limma$`PND15 vs Adult`
colnames(dea) <- paste("DEA", colnames(dea), sep = "_")
dea <- dea[abs(dea$DEA_logFC) >= 1 & dea$DEA_adj.P.Val <= 0.05,]
tf <- readxl::read_xlsx(path = "input/atac_diff_acc_tfbs_hocomoco_overlap.xlsx", sheet = 1, trim_ws = T)
Map with Genes
tab <- merge(tf, dea, by.y = "DEA_Genes", by.x = "TF-Transcription factor")
Save table
writexl::write_xlsx(tab, "./output/dea_genes_overlap_tf_motifs.xlsx", col_names = T, format_headers = T)
Plot for TF overlapping DEGs
plot_ly(
data = tab, x = tab$DEA_logFC, y = tab$`diffAccessibility-logFC`,
marker = list(size = 5, color = "blue"),
text = ~ paste(
"Gene: ", tab$`Peak-SYMBOL`,
"<br>Name: ", tab$`Peak-GENENAME`,
"<br>Annotation: ", tab$`Peak-annotation`,
"<br>DA logFC: ", tab$`diffAccessibility-logFC`,
"<br>DA FDR: ", tab$`diffAccessibility-qvalue`,
"<br>DE logFC: ", tab$DEA_logFC,
"<br>DE FDR: ", tab$DEA_adj.P.Val
),
hoverinfo = "text"
) %>%
layout(
title = "TF Motifs overlapping differentially expressed genes",
yaxis = list(title = "logFC: Differential Accessibility (DA)"),
xaxis = list(title = "logFC: Differential Expression (DE)")
)
SessionInfo
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.2 (2019-12-12)
## os Ubuntu 16.04.6 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/Zurich
## date 2020-01-16
##
## ─ Packages ───────────────────────────────────────────────────────────────────
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## callr 3.4.0 2019-12-09 [1] CRAN (R 3.6.1)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.6.1)
## cli 2.0.0 2019-12-09 [1] CRAN (R 3.6.1)
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## zeallot 0.1.0 2018-01-28 [1] CRAN (R 3.6.1)
##
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